It seems that my assumption of samba share not affecting at all is far to be true (http://www.samba.org/samba/news/symlink_attack.html
It's of course a matter of how I organize the files, but to be able to use soft links I must disable [unix extensions] and enable [wide links] directives on samba configuration. So if I want to stick with default samba configuration and consider both Windows and Linux clients, I must use hard links.
On the other side of investigation, I will not need to traverse anything due to the inhability of hardlinking directories. As application generates directories itself and inotify takes account of this, I can make directories as soon as application does. And cp -al comes to the rescue as an one-for-all solution making dirs and linking files as desired.